A Bitter Brew Indeed
by Protectress of Dalidon
Summary: After a deal is made, Shepard takes Weir offworld as the fourth in his team. Once things go wrong, and they make it back to Atlantis, Weir changes and it's up to Shepard to fix things, if he can... ShWeir, Angst, possible spoliers.
1. Prologue

A/N: I own nothing, but isn't the universe a great place to play? And I promise that I won't let anyone die for extended periods.

For my dearest friend and muse.

0o0o0o0o0o0o0

Shepard looked at her and wanted to shake her, gently of course. They were on the balcony, so he took the liberty of raising his voice a little.

'How can you say that you know a damn thing about off-world missions?'

'I've read your reports John, I read all the reports, and I'm telling you, if you don't start taking less risks, I am going to seriously reconsider sending your team off-world.' Considering they had nearly died last time, again, Weir was serious. And Shepard knew it.

'You can't do that!' There was a moment of silence, and he realized he'd said the wrong thing to the most powerful woman in Atlantis.

'If I believe it's better for Atlantis, I will.'

John licked his lips and shifted his weight, changing tactics. 'Look, I'm not saying that you don't understand, I'm just saying you've got all the theory and none of the prac.'

'I've been off-world John, I go whenever necessary. Generally in your company, remember?'

'But you don't ever go to a planet first, you're always there after someone's already checked it out. I'm not saying that it's a bad thing,' he added, raising his hand to still her retort, 'I'm saying that you haven't been exposed to the same risks my team takes every time we step through the gate.'

'Which is precisely why I'm considering suspending your activities.'

'I'll make a deal with you.'

'What?' Weir narrowed her eyes, tilted her head slightly and waited for his next move.

'I'll make a deal. You come with us on one mission, you weigh the risks and how we handle them without the benefit of hindsight. If you think it's still too risky to be worth what we can gain, I'll give up my team.'

'You'd do that?' she asked, her eyes narrowing slightly as she assessed him. She knew, just by the way he fidgeted slightly, tilted his head and tipped a shoulder in a half-shrug, that he'd given more than he'd planned. But that was the way he was, impulsive, instinctive, and that was what made him such a fine addition to Atlantis.

Weir raised her hand, offered it to him. 'Deal.' Shepard clasped her hand. 'But this is binding John. Atlantis needs you.' _I need you._ The words sat in the air until he nodded. The moment shattered as he stepped back and towards the control room.

'Be ready in an hour and meet us in the jumper bay.'

'I thought you weren't going out until Teyla got back from the mainland.'

John smiled. 'Got four in my team now, don't I?' He winked and left. Elizabeth watched him, a smile playing on the corner of her lips. She wondered who had been manipulating whom. Brushing the thought away, she headed into her office to set up a few things and make sure there were no issues that couldn't wait until she got back.

0o0o0o0o0o0o0

The gate activated and the control room staff leapt to their stations.

'Colonel Shepard's IDC.'

'Lower the shield!'

The wormhole showed blue and the jumper appeared, bringing a moment's relief.

'Dammit we need a medical team!' It was Shepard, his voice loud enough to echo around the gate room and reach the corridors, despite being over the radio.

'Medical team to the jumper bay.'

The wormhole disconnected as the jumper cleared the gate room. The control room staff looked at each other, still and pale. They had never heard that particular tone of concern, demand and anger in his voice before. Someone muttered a quick but fervent prayer.


	2. Subtle differences

_A/N: I own nothing and will put them all neatly back in the appropriate boxes once I'm done, promise.  
_

_ A speacial thank you to everyone who reviewed, here is the next installment. And don't worry, I wouldn't dare hurt Elizabeth, she is just too awesome! And yes, this is all because you moved, Charlie. If you were here, you'd already know what was going to happen..._

* * *

Carson looked over the test results for the third time and finally approached the woman leaning on the edge of one of the beds. She was meant to be sitting down but she was so used to being on the move that Carson assumed the stillness was stifling. He didn't smile as he reached her, closing the folder and holding it in front of him. 

'I'm so sorry love,' he said, the words soft enough that no one else would hear.

'You're sure?' She looked up at him, the last measures of hope fading from her green eyes. He'd always hated giving bad news, now more than ever.

'Aye love, I'm positive, and at this stage, since we don't know what caused it, I don't know of a cure.' He could almost feel the weight of that knowledge falling on her shoulders and he silently cursed himself. Why did he tell her that? She had enough to deal with already.

'I understand,' she said, her voice hollow, 'is there anything else?'

Carson shook his head. 'Although, I'd strongly suggest you talk to-'

'I'll make an appointment.' She inclined her head slightly, the same way she ended conversations, and a moment later, she was walking out of the infirmary and back to the command centre of the Atlantis base. Carson sighed, the file against his chest. He knew that she wouldn't go and see Kate, she'd make the appointment and something would come up. Although if she did go, she'd give all the right responses and there would be nothing that anyone could do to help her. That had been a complaint he'd heard from the other doctor on and off since they'd arrived, really. It was a well-established fact that any kind of assistance with emotionally or mental issues was hampered by the patient being clever. Weir could manipulate words until they were still telling the truth, but they had no relevance at all. Shaking his head, Carson decided that it was definitely in the best interests of everyone on Atlantis if someone kept and eye on Weir. The real question was who…

On her way back to her office, a change seemed to settle over the leader of Atlantis, although it was a subtle thing at first. It began with the way she stood, her body curling in on itself slightly as though wounded, then her arms crossed defensively, her footfalls shifted from confident to wary. She lowered her head, the strands of dark brown hair falling across her face as she paused. It was only a moment, and there was no one to see that instant of vulnerability before it disappeared and she stood tall again. She walked back to the control room, her strides even and purposeful. Since everyone was busy, no one noticed the change immediately. It was her eyes that gave away the shift. Once they had been easy to read, they now resembled green slate, hard and still. Her normal warmth had been replaced with the sense of sun kissed marble, walls created without doors. And it would only be a fool who thought to tease her into a good humour, or test the limits of her orders. She picked up her data pad and started making notes.


	3. Dividing

_A/N: I own nothing, I will put them all back when I'm done, I promise..._

_Just to clear a few thing up, the first chapter is a prologue, so pretend the opening credits start to roll. And I'm hoping this chapter clears up a few questions, and raises a whole lot more. Angst and Intrigue are my current helpers... I hope you have as much fin reading this chapter as I did writing it, and I love Sparky cookies!!  
_

_To my dearest friend and muse, as always._

* * *

Weir was back in her office and reading through one of the mission reports when John walked in. He didn't expect her to look up, and she didn't, but he had expected some acknowledgement of his presence. She didn't move. 

'Elizabeth?' he said after the silence began to worry him.

'Mmmm?' she replied without lifting her gaze from the report. It was clear that she was reading it, but he couldn't remember a time when she hadn't at least looked at him.

'I just thought I'd drop by and-'

'I'm fine.' Her voice was even, calm, but still he leant back on his heels a little. And he knew that she had never sounded so… not fine, in all his time on Atlantis. Well, maybe that time with the storm, and the time he'd taken a 'jumper and a nuke… Okay, he admitted, she'd sound not fine a lot, but never the way she did at that moment.

'Right,' he said, nodding, 'good, then I'll go see what Rodney's doing.' He turned on his heel.

'Dr McKay is working on some very important experiments and I'd prefer you didn't interrupt him.' Still, she didn't look at him.

'Okay,' John said, 'I'll go find Teyla and Ronon.'

'Teyla is on the mainland getting a trade consignment ready and Ronon is running through some drills with the marines.'

John turned and faced her, eyes alight with confused frustration. 'Why wasn't I told about this?'

'Because you were off visiting some of our _allies_ when the meeting was held.' The emphasis on the word made it clear whom she was referring to. John winced. He remembered that conversation over the radio. Considering he'd already started the dialing sequence and Elizabeth wouldn't have raised the shield on him, he hadn't really thought about the meeting any further. Obviously, she had.

'And what was decided in the meeting?' His voice held the edge of his frustration. Finally, Weir raised her eyes to his and the coldness in them shocked him. She didn't smile as she spoke.

'The temporary reassignment of Dr Rodney McKay and Specialists Teyla Emmagon and Ronon Dex, which you would have known if you had read the memo I sent you.'

John opened his mouth to say her name and then looked at her, really looked at her. What he saw was enough to silence his instinctive arguments. This woman sitting behind Dr Elizabeth Weir's desk was not the same woman who had accompanied him on the mission they'd returned from three days earlier.

'And my new assignment?' The words almost stuck in his throat, but he had to ask.

'As you are the military leader of this expedition, I believe it would be best if we discussed a change in duties. Unfortunately, during my absence, the necessary work to run the _civilian_ part of the expedition seems to have been overlooked. You have downtime until what counts as next week.' Her gaze didn't waver, her voice didn't tremble, she was as calm as she had been at the beginning of the conversation and it was John who lost his composure. He walked out, mentally cursing every god he had ever heard about. Something was wrong, something was really wrong and he needed to find out what. With that in mind, he stalked through the corridors, keeping the words of Weir, he couldn't think of her as Elizabeth, in mind. That left him one real option, and he headed straight for Atlantis' version of hell.

0o0

In her office, Weir continued to pretend to read the report, her eyes merely scanning the words before her. She'd read it already, over and over again. Still, there were no clues in the document and she put it down with a sigh. What had she been hoping for, some detail to trigger a memory clouded with strangers' faces and strange smells and a pain she couldn't bear because she somehow knew what it meant? Just like she'd known that Carson wouldn't be able to give her good news, she knew she would be best to move on. It was a small thing really, and considering she was the leader of a people who lived each day in apprehension if not fear, it was a small thing. But still, its weight was a heavier burden than she had faced thus far. She ran a hand down her arm thoughtlessly. Taking a deep breath, she picked up one of Lorne's reports and began to read.


	4. Secrets and Stories

_A/N: I own nothing and will put them back when I'm done..._

_Thanks to everyone who reviewed, it means a lot to me. And I hope this chapter answers some questions._

_Dedicated, as always, to my dearest friend and muse._

* * *

'She's where?' Carson demanded, spinning to face the very annoyed John.

'In her office, and I tell you, something is definitely not right-'

'Bloody oath it's not,' the doctor replied, practically slamming a file into it's place, 'I told her she was to have the rest of the week off, not go back to that damn tower of hers.' For the first time, John got to see what Carson was like after one of his patients tried to escape.

'I could go and remind her for you,' John offered, aware that something was going on, and if he just asked the right questions he might get answers.

'I don't think so lad.' Carson seemed to be getting control of his temper, and John realised that he mightn't be able to pry information from the man. Sometimes professionalism just got in the way… well, in his way at any rate.

'If it's something that concerns the running of the city-'

'It's not. Like you, she's on a break under medical advice.' Carson didn't smile as he tapped the radio at his ear and paged Weir. 'You better find something to do,' the doctor said to John once his was message delivered, 'because she's not going to want to see you.'

'She reassigned my team without consulting me, I don't want to see her,' John retorted. Carson shook his head.

'Son, you were the one who convinced her that the risks were worth it, that you'd be fine. She kept her side of your deal, stop acting like a bairn because you have to hold up your end.'

'She told you about that?'

'Aye, considering that she had no reason to go to that damn planet, I insisted on an explanation as soon as she was conscious.'

That made John hesitate. 'I was there when she woke up…'

'No, lad, you weren't. And she won't want you here now, so I suggest you get some lunch.'

'Carson, what happened to her?'

'I don't know exactly, but it happened on the planet, and she's put it on the prohibited list.'

'But the natives have a whole heap of stuff you and the medical researchers should see!'

'Aye lad, and if I could go and just get a sample of whatever it was they were feeding her…' Carson shook his head, his eyes showing the first hints of subversive intent.

'You think her allergic reaction was due to the food?' he asked gently.

'It wasn't an allergic reaction that put her into a semi-comatose state, Elizabeth doesn't have allergies, and nothing does that, not even in Pegasus.' Carson was irate. Without realising it, John had touched on the very point that mattered.

'You're saying they drugged her.'

Carson nodded. 'Aye lad, and for what purpose I don't know. But I ran your blood work, and Rodney's and Ronon's, and there were distinct lacks of some elements found in Elizabeth's blood. Since you all ate and drank the same thing, I just can't account for it.' He shook his head. 'And now I won't even be able to get samples to run, because that damned planet is off-limits.' Running a hand over his face, Carson finally got a hold of himself. 'Now, you go amuse yourself, Ronon should be finished with the marines, and Rodney will have made a break for the commissary, or I don't know the man at all.' With a smile to John, the doctor picked up his folder and headed for the door, undoubtedly to await Elizabeth's arrival. John watched him go, his rage held in check by the thinnest strand of common sense that had ever prevailed upon him. He'd thought it was only incredibly bad luck that Elizabeth had gotten so sick on the planet… Now what some of the villagers had said started to make sense. They'd been very tight-lipped about what was going on, hadn't let the team do more than bare minimum first aid checks. And they hadn't been allowed to draw blood. Walking out of the infirmary without smashing something was the hardest thing John had ever had to do, after not searching for Elizabeth's hardcopy file. Things were starting to make sense in a horrible way. He smiled, that same smile that touched his lips when he was planning something. With an expression that cleared hallways, he headed to the mess hall bay, intent on acquiring some assistance for his next mission. Sometimes, Elizabeth made decisions early and couldn't back out of them when she needed to…

0o0o0o0

'What crazy plan do you have in mind now?' Rodney asked as John sat down. Actually, the words were a bit distorted because of the amount of food in the physicist's mouth, but that was the general meaning. John understood simply because he had spent far too much time with the man.

'How's the research going?' John asked, ignoring the question and lifting his turkey sandwich to his lips. There were times when subtly was helpful. Besides, Ronon wasn't there yet and John didn't want to repeat himself.

Rodney shook his head. 'Terrible, the interface won't work properly and there's no way we can get the power frequencies to match. I hate to admit it, but Zalenka was right, it's a waste of time.'

'Really? How much more time did Elizabeth give you to work on it?'

'As long as it takes. Unlike some other leaders, she's actually been really good about it… Although I'm looking forward to an off-world mission. If I have to spend another minute with that paranoid, pony-tailed moron, I could be incited to violence and we all know that never ends well for me.' Rodney crammed more food into his mouth as John blinked at him. He'd known the man had changed since they'd come to Atlantis, but he'd never realised how much… But then again, once the team had found out that instead of a letter home Kavanagh had sent a list of all Elizabeth's perceived transgressions, tempers had certainly been stretched. 'Oh, and how was your visit with Chaya? I know that you missed the big meeting for it, so it must have been important…'

'I was thinking, we should go back to the planet,' John replied, ignoring the last statement as best he could.

'Chaya's? Why? It's not like she can help us, stupid Ascended rules…'

'He meant back to our last mission,' Ronon supplied, appearing suddenly and taking a seat.

'How are the marines?' John asked.

'Slow, and they think their shooting skills are brilliant.' Ronon rolled his eyes.

'Probably couldn't hit the broadside of a barn,' Rodney added in between mouthfuls. 'And why would we go back to that horribly primitive, superstitious place anyway? I mean, they have interesting ideas on population control, and it seems to be more effective than suicide pacts, but it gives me the creeps.'

'Did you figure out how they did it?' Something tugged at the back of John's mind and he tried to grasp it, but it slipped away like silk in the breeze.

'Do I look like an anthropologist? No, I have no idea, I just know that it wasn't part of an advanced culture.'

'Maybe we should go ask them.' It wasn't a question from the Satedan. Ronon had alluded at the time that being part of the Satedan military was different than the Earth one, but wouldn't elaborate. John had a feeling the quietly intense suggestion had a lot to do with the man's past. And John didn't mind. Here was an ally, and between the two of them, they could always carry Rodney into the 'jumper…

'We really should take Carson then,' Rodney said, 'see if he can figure anything out.' The other men stared at him, Ronon even pausing in the consumption of food. John opened his mouth to respond but was silenced. 'What? You think that you or me or Conan here know enough about voodoo to figure it out?'

'You should stop calling him Conan.'

'And you should stop having intimate relations with alien women, but I don't see that happening in the near future.' There was a pause as Rodney shook his head. 'Anyway, if we're going to kidnap Carson, we should get on with it. After all, he goes off duty in about,' Rodney looked at his watch, 'ten minutes, and we'll want to nab him then.' With that, he stood and picked up his half-full tray. The others didn't move, just stared at him as though he had grown an extra head. 'What? I'm not allowed to be concerned about the wellbeing of our esteemed leader?'

'You're not supposed to come up with brilliant plans without the threat of impending doom,' John corrected, getting to his feet.

'If we don't figure this out, he'll never get out of the lab,' Ronon said, shaking his head as he too abandoned his meal.

'And considering who I have to work with, except Zalenka of course, it counts as impending doom. I know we don't have a capital punishment system, but I figure pushing someone through the Stargate so they come out in hard vacuum would probably get me in trouble. Actually,' Rodney said, wandering off a little, 'it might get me commended…' No one really liked Kavanagh, after all…

'How about we just have one plan at a time, what do you say?' John offered, striding towards the exit.

'Sounds good to me,' Ronon muttered, 'too many plans and _we'll _end up in hard vacuum.' With that, the men walked out, heading for the infirmary. They were the objects of many confused glances, but they ignored them all. Kidnapping the Chief Medical Officer was a much more important consideration than how people looked at them.

0o0o0o0

Elizabeth had retreated from the infirmary well and truly before the trio arrived, and had headed for her room. If there was one thing she couldn't handle, it was an irate Carson. He did so much for them that she couldn't, in clear conscience, put more pressure on him by misbehaving. So she headed for her room, expecting to reach it, and the book she was reading for the twelfth time, in peace. Suddenly, someone came running down the corridor, holding what looked to be an Ancient design tablet. Elizabeth could see the joy on the young woman's face, and although she couldn't remember the scientist's name, she smiled too. When she saw Elizabeth, the young woman holding the tablet skittered to a stop and grinned.

'Oh, Dr. Weir, I've been looking for you all over,' the young woman said, ridiculously excited.

'Really? Has something happened?' Elizabeth asked, expecting the worst.

'Yes, we've found a whole room full of these.' She waved the tablet. 'And since you're the foremost expert on Ancient language, I thought you might want to read it.' The young woman handed the tablet over and pointed to one of the ornate buttons on the side. 'That should turn it on. Oh, I think you're really going to like it.' With a grin and a wave, the young woman was gone, leaving Elizabeth outside her room, holding a tablet that she had no idea about. Shaking her head, Elizabeth palmed open her door and went inside, touching the button and reading over the first few lines that appeared on the screen. The door closed, shutting off the sob that echoed in Elizabeth's room as she translated.

Once upon a time, there was a city that sat on the ocean like a lily on a pond. In that wondrous place lived a little girl and her parents. Her mother was renowned for her skill with words and her father was a mighty warrior. The little girl was very happy, and loved her family very much. Almost as much as they loved her.

Elizabeth slowly sunk to the floor, the tablet slipping from her fingers and landing with a quiet thud. Wrapping her arms around her middle, Elizabeth leant her head on her up-drawn knees and wept. The tablet glowed in the darkness.


End file.
